NMRFAM is active in the development of software tools that facilitate investigations by NMR.  Advanced computational analysis algorithm research, new methods integration, user interface development, and instrument automation are combined to increase the accessibility, accuracy and efficiency of the range of methodologies employed.  The software packages shown below are developed or supported at NMRFAM, and are available for download or remote use on our servers and spectrometers.

 

NMRFAM Webservers

[Go to the NMRFAM Webservers]

NMRFAM Software Tools

[Go to the universal NMRFAM Software download page]

ADAPT-NMR

Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR: a fully automated method for integration of optimized protein NMR data collection, chemical shift assignment, and secondary structure determination. PUBLICATION

ADAPT-NMR Enhancer

Software for visualization and analysis of tilted plane spectra derived from ADAPT-NMR. PUBLICATION

ARECA

ARECA (Assessment of the REliability of Chemical shift Assignments): A probabilistic validation of protein NMR chemical shift assignments against NOESY data . PUBLICATION

HIFI-NMR

High-resolution Iterative  Frequency Identification for NMR: an adaptive approach for rapid and automated collection of NMR data. PUBLICATION

LACS

Linear Analysis of Chemical Shifts: a method for detection and automated correction of potential referencing problems and detection of inconsistent assignments  - now included in PINE! PUBLICATION

Newton

Spectral analysis of multidimensional NMR data useful for complex mixtures. Newton implements a Fast Maximum Likelihood Reconstruction (FMLR) of NMR spectra from spectral deconvolution of raw data that constructs the simplest time-domain model whose fourier processed spectrum most closely matches the spectrum of the identically processed FID. PUBLICATION

NMRbot

High throughput data acquisition for Bruker NMR spectrometers running Topspin >2.0, fitted with ATM and SampleJet hardware accessories. PUBLICATION

NMRFAM-SPARKY

SPARKY supports user-defined enhancements, and we have used these to develop new tools in support of our packages for automated protein assignment and structure determination. The added features support (1) interfacing with servers offering new technologies, (2) tools for data visualization and verification, and (3) new protocols for maximizing the efficiency of NMR data analysis. PUBLICATION
 NMR Structure Tools
 A PyMol add-on with tools for NMR structure ensemble analysis such as pairwise alignment, structure restraint validation and hydrogen-bond detection.

PACSY

Protein structure And Chemical Shift NMR spectroscopY: a relational database management system that integrates information from the Protein Data Bank (PDB), the Biological Magnetic Resonance Data Bank (BMRB), and the Structural Classification of Proteins (SCOP) database. PUBLICATION

PECAN

Protein Energetic Conformational Analysis from NMR chemical shifts: probabilistic secondary structure predictions from chemical shift– now included in PINE! PUBLICATION

PINE

Probilistic Interaction Network of Evidence: a probabilistic algorithm for automated backbone and sidechain assignments, with detection and correction of referencing and secondary structure determination from input protein sequence and NMR data set peak lists. PUBLICATION

PINE-Sparky

SPARKY extension for the manual verification of PINE automated assignments. Now included in the NMRFAM-SPARKY Distribution. PUBLICATION

PONDEROSA

PONDEROSA-C/S

Peak picking Of NOE Data Enabled by Restriction Of Shift Assignments: a program for protein structure determination that utilizes information from prior assignments to automatically pick NOE peaks from 3D-NOESY (13C-edited and 15N-edited) spectra, with results used as input for a series of CYANA structure calculations. PUBLICATION

PONDEROSA-C/S builds on the original PONDEROSA software and includes improved features for structure calculation and refinement in client-server model. PUBLICATION

RNA-PAIRS

RNA Probabilistic Assignment of Imino Resonance Shifts: a probabilistic algorithm for the automated assignment of RNA imino 1H and 15N resonances shifts, with conjoined determination and validation of secondary structure from input RNA sequence, and 1H-1H 2D-NOESY and 1H-15N 2D-HSQC spectra peak lists. PUBLICATION

rNMR

An open source software package for visualizing and interpreting one and two dimensional NMR data specifically designed for high-throughput assignment and quantification of small molecules. Supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks. PUBLICATION

NMRFAM Script Library

A collection of scripts for NMR spectroscopists and general macromolecular structure research.
NMRFAM Virtual Machine

Ubuntu Mate based Virtual Machine (VM) with pre-installed the latest versions of NMRFAM-Sparky, PyMOL, PONDEROSA-C/S packages.

A VM is an emulation of a computer operating system that can be installed and run on any different operating system. NMRFAM's VM runs the Linux operating system Ubuntu. To run this on your Windows, Mac, or Linux computer, you will need to install VirtualBox (a virtualization software package from Oracle, freely available at www.virtualbox.org). You MUST have administrative privileges to install VirtualBox on your computer. For PCs, VirtualBox requires the enabling of virtualization in the BIOS.

NMRmix

A tool for the optimization of compound mixtures in 1D 1H NMR ligand affinity screens. PUBLICATION

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Biochem 800 – Practical Nuclear Magnetic Resonance Theory

Biochem 801 – Biochemical Applications of Nuclear Magnetic Resonance

"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Workshop "Ultrahigh Field NMR and MRI: Science at a Crossroads" November 12-13, NIH

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 

 

Donate to NMRFAM. US tax-deductible donation can be made to NMRFAM
Please write check payable to "UW Foundation, Account 112152802"  
And mail to: 
Attn: Sarah Lynn Traver Saunders
Associate Administrative Program Specialist 
University of Wisconsin-Madison 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 

 

1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

3rd: Mark Anderson
Rm B224; Phone 265-3303

4th: Marco Tonelli
Rm B160; Phone 263-9493

5th: John Markley
Rm 171A; Phone 263-9349

We welcome your questions and feedback!

NMRFAM Established 1987